Hi all, so I'm experiencing a problem running SAM-to-BAM using samtools 1.2 from a toolshed install of suite_samtools_1_2. I have a pipeline that after mapping uses 'SAM-to-BAM', followed by GATK2 'realign target creator/indel realign' and then picard 'mark duplicate reads'. When I run this last picard step I am getting the EOF marker absent error. This problem seems to be confined only to when I run the pipeline with an inbuilt genome build I created (I created all loc files and index files).
I am running the 15_05 stable release from git. Is it possible that I have malformed index files for this genome or is this something to do with the way that Galaxy is now indexing the BAM file?
Any help/suggestions greatly appreciated as I have been stuck with this issue for a few days now.
[bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file.